LAIT: a local ancestry inference toolkit.
LAIT: a local ancestry inference toolkit.
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DOI：
10.1186/s12863-017-0546-y
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发表时间：
2017-09-06
期刊：
影响因子：
2.9
通讯作者：
Chen W
中科院分区：
文献类型：
--
作者：
Hui D;Fang Z;Lin J;Duan Q;Li Y;Hu M;Chen W
推断混合血统个体的本地血统有许多应用，最显著的是在确定不同种族群体之间不同的疾病易感位点。许多软件包可用于推断混合个体的本地血统。但是，大多数现有的软件包都需要特定的格式化输入文件，并生成各种类型的输出文件，这给实际操作带来了不便。我们开发了一个工具集，本地祖先推理工具包（LAIT），它可以将标准化文件转换为特定于软件的输入文件格式，并对四种流行的本地祖先推理软件（HAPMIX， LAMP， LAMP- ld和ELAI）的推理结果进行标准化和汇总。我们使用模拟和真实数据集对LAIT进行了测试，并证明了LAIT为运行多个本地祖先推断软件提供了便利。此外，我们在不同支持的软件包中评估了本地祖先软件的性能，主要关注推理精度和使用的计算资源。我们提供了一个工具包，以方便使用本地祖先推断软件，特别是对有限的生物信息学背景的用户。本文的在线版本（doi:10.1186/s12863-017-0546-y）包含补充材料，可供授权用户使用。
Inferring local ancestry in individuals of mixed ancestry has many applications, most notably in identifying disease-susceptible loci that vary among different ethnic groups. Many software packages are available for inferring local ancestry in admixed individuals. However, most of these existing software packages require specific formatted input files and generate output files in various types, yielding practical inconvenience. We developed a tool set, Local Ancestry Inference Toolkit (LAIT), which can convert standardized files into software-specific input file formats as well as standardize and summarize inference results for four popular local ancestry inference software: HAPMIX, LAMP, LAMP-LD, and ELAI. We tested LAIT using both simulated and real data sets and demonstrated that LAIT provides convenience to run multiple local ancestry inference software. In addition, we evaluated the performance of local ancestry software among different supported software packages, mainly focusing on inference accuracy and computational resources used. We provided a toolkit to facilitate the use of local ancestry inference software, especially for users with limited bioinformatics background. The online version of this article (doi:10.1186/s12863-017-0546-y) contains supplementary material, which is available to authorized users.
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影响因子：
64.8
作者：
Frazer, Kelly A.;Ballinger, Dennis G.;Cox, David R.;Hinds, David A.;Stuve, Laura L.;Gibbs, Richard A.;Belmont, John W.;Boudreau, Andrew;Hardenbol, Paul;Leal, Suzanne M.;Pasternak, Shiran;Wheeler, David A.;Willis, Thomas D.;Yu, Fuli;Yang, Huanming;Zeng, Changqing;Gao, Yang;Hu, Haoran;Hu, Weitao;Li, Chaohua;Lin, Wei;Liu, Siqi;Pan, Hao;Tang, Xiaoli;Wang, Jian;Wang, Wei;Yu, Jun;Zhang, Bo;Zhang, Qingrun;Zhao, Hongbin;Zhao, Hui;Zhou, Jun;Gabriel, Stacey B.;Barry, Rachel;Blumenstiel, Brendan;Camargo, Amy;Defelice, Matthew;Faggart, Maura;Goyette, Mary;Gupta, Supriya;Moore, Jamie;Nguyen, Huy;Onofrio, Robert C.;Parkin, Melissa;Roy, Jessica;Stahl, Erich;Winchester, Ellen;Ziaugra, Liuda;Altshuler, David;Shen, Yan;Yao, Zhijian;Huang, Wei;Chu, Xun;He, Yungang;Jin, Li;Liu, Yangfan;Shen, Yayun;Sun, Weiwei;Wang, Haifeng;Wang, Yi;Wang, Ying;Xiong, Xiaoyan;Xu, Liang;Waye, Mary M. Y.;Tsui, Stephen K. W.;Wong, J. Tze-Fei;Galver, Luana M.;Fan, Jian-Bing;Gunderson, Kevin;Murray, Sarah S.;Oliphant, Arnold R.;Chee, Mark S.;Montpetit, Alexandre;Chagnon, Fanny;Ferretti, Vincent;Leboeuf, Martin;Olivier, Jean-Franccois;Phillips, Michael S.;Roumy, Stephanie;Sallee, Clementine;Verner, Andrei;Hudson, Thomas J.;Kwok, Pui-Yan;Cai, Dongmei;Koboldt, Daniel C.;Miller, Raymond D.;Pawlikowska, Ludmila;Taillon-Miller, Patricia;Xiao, Ming;Tsui, Lap-Chee;Mak, William;Song, You Qiang;Tam, Paul K. H.;Nakamura, Yusuke;Kawaguchi, Takahisa;Kitamoto, Takuya;Morizono, Takashi;Nagashima, Atsushi;Ohnishi, Yozo;Sekine, Akihiro;Tanaka, Toshihiro;Tsunoda, Tatsuhiko;Deloukas, Panos;Bird, Christine P.;Delgado, Marcos;Dermitzakis, Emmanouil T.;Gwilliam, Rhian;Hunt, Sarah;Morrison, Jonathan;Powell, Don;Stranger, Barbara E.;Whittaker, Pamela;Bentley, David R.;Daly, Mark J.;de Bakker, Paul I. W.;Barrett, Jeff;Chretien, Yves R.;Maller, Julian;McCarroll, Steve;Patterson, Nick;Pe'er, Itsik;Price, Alkes;Purcell, Shaun;Richter, Daniel J.;Sabeti, Pardis;Saxena, Richa;Schaffner, Stephen F.;Sham, Pak C.;Varilly, Patrick;Altshuler, David;Stein, Lincoln D.;Krishnan, Lalitha;Smith, Albert Vernon;Tello-Ruiz, Marcela K.;Thorisson, Gudmundur A.;Chakravarti, Aravinda;Chen, Peter E.;Cutler, David J.;Kashuk, Carl S.;Lin, Shin;Abecasis, Goncalo R.;Guan, Weihua;Li, Yun;Munro, Heather M.;Qin, Zhaohui Steve;Thomas, Daryl J.;McVean, Gilean;Auton, Adam;Bottolo, Leonardo;Cardin, Niall;Eyheramendy, Susana;Freeman, Colin;Marchini, Jonathan;Myers, Simon;Spencer, Chris;Stephens, Matthew;Donnelly, Peter;Cardon, Lon R.;Clarke, Geraldine;Evans, David M.;Morris, Andrew P.;Weir, Bruce S.;Tsunoda, Tatsuhiko;Johnson, Todd A.;Mullikin, James C.;Sherry, Stephen T.;Feolo, Michael;Skol, Andrew
通讯作者：
Skol, Andrew
影响因子：
12.3
作者：
Zakharia F;Basu A;Absher D;Assimes TL;Go AS;Hlatky MA;Iribarren C;Knowles JW;Li J;Narasimhan B;Sidney S;Southwick A;Myers RM;Quertermous T;Risch N;Tang H
通讯作者：
Tang H
DOI：
10.1093/bioinformatics/btp197
发表时间：
2009-06-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Pasaniuc B;Sankararaman S;Kimmel G;Halperin E
通讯作者：
Halperin E
影响因子：
9.8
作者：
Bryc K;Durand EY;Macpherson JM;Reich D;Mountain JL
通讯作者：
Mountain JL
影响因子：
5.8
作者：
Baran, Yael;Pasaniuc, Bogdan;Halperin, Eran
通讯作者：
Halperin, Eran